From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Fri Feb 24 2017 - 11:46:32 CST
Thanks Jerome for the input. That really helped.
Giacomo, thanks for the explanation. I initially benchmarked my system on
NAMD 2.12 which went fine. And then I saw problems in NAMD 2.10 and was
quite confused. I have been in touch with Sunhwan, hopefully they will be
able to get their patch to work for NAMD 2.12.
Best regards,
Chitrak.
On Thu, Feb 23, 2017 at 10:58 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> Hi Chitrak, I presume that you know that in NAMD 2.12, Colvars now uses
> the NAMD's internal functions that compute centers of mass in a parallel
> fashion (as also done in tclForces). They will still carry a bit of
> overhead, but it's not bad unless you request something like the entire
> system.
>
> If you need REST2, you may want to ask Sunhwan and Wei to invest some
> effort into porting the patch to the current NAMD. There are several
> innovations in newer versions of NAMD that do not make it worth sticking to
> an old one.
>
> Giacomo
>
> On Thu, Feb 23, 2017 at 6:36 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
> wrote:
>
>> Hi,
>>
>> Your problem is entirely the number of atoms. if you pick just one atom
>> per lipid (e.g. a glycerol carbon), you should get the same center position
>> at a much reduced cost.
>>
>> Best,
>> Jerome
>>
>> On 24 February 2017 at 00:25, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:
>>
>>> Hello,
>>>
>>> I am doing solute tempering simulations with a POPC/peptide system using
>>> NAMD 2.10. To the best of my knowledge, this is the only version of NAMD
>>> that can work with the REST2 implementation (Jo and Jiang, JCTC, 197:304,
>>> [2015])
>>>
>>> I also have 3 colvars to prevent my peptide from interacting with the
>>> lipids in the periodic image along Z dimension. These are distance colvars,
>>> defining the distance of the N-terminal residue, center residue, and
>>> C-terminal residue with the lipid heavy atoms. Number of atoms in each
>>> colvar is ~ 10500.
>>>
>>> From what I understood from the following link, it is the number of
>>> colvars and not number of atoms in a colvar that could affect the scaling,
>>> correct?
>>>
>>> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.201
>>> 3-2014/1135.html
>>>
>>> Has anyone else faced this issue? And any suggestions on how best to
>>> address this? Would using the absolute Z value of the residues as the
>>> colvar give the same effect with a better scaling?
>>>
>>> Thanks and regards,
>>> Chitrak.
>>>
>>
>>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>
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